Detection, Visualization and Quantification of Protein Complexes in Human Alzheimer’s Disease Brains using Proximity Ligation Assay

Examination of healthy and diseased human brain is essential to translational neuroscience. Protein-protein interactions play a pivotal role in physiological and pathological processes, but their detection is di cult, especially in aged and fixed human brain tissue. We used the proximity ligation assay (PLA) to broaden the range of molecular interactions assessable in-situ in human neuropathology. We adapted fluorescent in-situ PLA to detect ubiquitin-modified proteins in human brains with Alzheimer’s disease (AD), including approaches for the management of auto fluorescence and Quantification using a high-content image analysis system. We confirmed that hyperphosphorylated microtubule-associated protein tau (Serine202, Threonine205) aggregates were modified by ubiquitin and that phospho-tau-ubiquitin complexes were increased in hippocampal and frontal cortex regions in AD compared to non-AD brains. Overall, we refined PLA for use in human neuropathology, which has revealed a profound change in the distribution of ubiquitin in AD brain and its association with characteristic tau pathologies.


Introduction
Traditional histological techniques have been central to visualizing cellular connections and understanding the function of the brain. These approaches were fundamental to Dr. Alois Alzheimer's discovery of his eponymous disease and formed the core of Santiago Ramón y Cajal's Nobel prize winning work in the early part of the 20th century. With the advent of immunohistochemical methods and progressively more re ned microscopy platforms, the degree of molecular information that can be derived directly from intact brain is progressively expanding. However, interrogating protein-protein interactions (PPIs) and post-translational modi cations (PTMs) of proteins in-situ in the brain remains di cult (1,2). Consequently, many disease mechanisms are primarily studied in cellular and animal model systems. Nevertheless, con rming that potential disease mechanisms are relevant in their appropriate context in neuropathological studies remains critical to interrogating the molecular mechanisms of brain diseases in translational neuroscience. Moreover, PPIs are potential targets for therapeutic drugs, so visualization and quanti cation of PPIs may be a useful tool in drug discovery and development (3,4,5,6).
The proximity ligation assay (PLA) is a technique used to study PPIs that was described twenty years ago (7) and was rst applied to detect PPIs in cultured cells in 2005 (8, 9). The approach produces a punctate uorescent focus when two antibodies bind targets near each other. Each antibody in the pair is conjugated to complementary oligonucleotides. These oligomers can hybridize to form circular DNA that serves as a template for ampli cation which is hybridized with a brightly uorescent-labeled oligonucleotide complementary to the ampli ed rolling circle product (10,11,12,13). The resulting signal implies the two antibody probes are close enough that their targets likely form a protein complex. The maximal distance between the two antibodies that can generate a signal is estimated to be between 15 and 40 nm depending on the size of the oligomers and whether primary antibodies are directly conjugated to the oligomer, or if conjugated secondary antibodies are used. This range is comparable to (albeit slightly larger than) the proximity resolvable using Fluorescent Resonance Energy Transfer (FRET), but with superior sensitivity for low-abundance proteins (14). Use of the uorescent PLA format in human brain tissue has been limited due to the extent of auto uorescence and non-speci c signals. In this technical report, we aimed to re ne the PLA methodology for use in human brain to expand the range of protein-protein interactions which can be evaluated in-situ in human neuropathology. To do that, we visualized the ubiquitination of a phosphorylated form of tau protein.
Age-related changes in the brain, along with genetic, lifestyle and environmental factors can promote the accumulation of modi ed tau species in neurons. These changes are most dramatic in Alzheimer's disease (AD) and related tauopathies (15,16,17). Because neuro brillary tangles (NFTs), large intraneuronal aggregates of hyperphosphorylated tau, strongly correlate with cognitive symptoms in AD, tau pathology can be considered a major toxic factor promoting neuronal network failure and neurodegeneration (18,19,20).
Aggregated tau is known to undergo several post-translational modi cations (21) including acetylation (22,23), methylation (24,25), SUMOylation (26) and ubiquitination (23,24,27,28,29). However, the signi cance of these modi cations in diseased human brain tissue remains unclear due to the lack of methods which can allow their subcellular localization, detection, and quanti cation. For example, the role of polyubiquitination in the complex pathways associated with tau aggregation and propagation is incompletely understood but may contribute to axonal failure in AD. Developing advanced molecular imaging tools to visualize this process in the brain and characterize tau ubiquitination or other protein complexes may provide critical insights into the biology of AD brain.
In this study, we describe a new approach that make the uorescent PLA suitable for human neuropathology applications. Bran tissue preparation Human brain tissue was obtained at autopsy and immersed in 10% formalin (ThermoFisher Scienti c, Pittsburgh, PA) at 4 o C for 1-3 days. The xative solution was then removed and the tissued rinsed with 1x TBS (Corning, New York, NY) three times for 5 minutes each. The tissue was placed in sterile 10% sucrose (Sigma-Aldrich, St. Louis, MO) /1x TBS/0.02% sodium azide (NaN 3 , Sigma-Aldrich) until tissue sank and then 30% sucrose/1x TBS/0.02% NaN 3 for overnight at 4 o C or until the tissue sank.

Human brain tissue
The tissue block was a xed to the stage of vibratome using cyanoacrylate cement and fully submerged in 1x TBS. Hippocampal and frontal cortex sections were prepared at 50 µm thickness. Floating tissue sections were transferred to 15 mL Falcon tubes with antigen retrieval buffer (10 mM citric acid pH 6.0 (Sigma-Aldrich) containing 0.05% Tween-20 (Sigma-Aldrich)) and heated to 95˚C for 20 minutes in the block heater. Sections were then washed with 100 mM glycine (Sigma-Aldrich)/1x TBS/0.1% Triton X-100 (Sigma-Aldrich) buffer for 30 minutes followed by permeabilization with 0.3% Triton X-100/1x TBS buffer for 30 minutes and two washes for 5 minutes each with 1x TBS at room temperature.

Proximity Ligation Assay and immunohistochemistry
Protein-protein interaction assessment in postmortem human brain was performed using the Duolink® Proximity Ligation Assay (PLA) kit (Sigma-Aldrich), following the protocol as previously described (13,30) with some modi cations, and the Ubiquitin Recombinant Rabbit Monoclonal Antibody clone 10H4L21 (5 µg/mL, 701339; Invitrogen, Carlsbad, CA), and the Phospho-tau (Ser202, Thr205) Monoclonal Antibody (AT8) (5 µg/mL, MN1020; Invitrogen) that recognizes phosphorylated tau at serine 202 (Ser202) and threonine 205 (Thr205) and labels neuro brillary tangles (31,32,33). For alternative reagents and solutions see (13,30). The disappearance of auto uorescence was checked by uorescent microscopy before continuing the assay. Sections were then incubated with the primary antibodies at 4 o C overnight and washed four times for 10 minutes each with buffer A (1x TBS/0.05% Tween-20) under gentle agitation. Secondary antibodies/proximity probes were diluted with the same antibody diluent that was used for the primary antibodies and was applied to the sections for 90 minutes at 37 o C. Unbound proximity probes were removed by washing the samples four times for 10 minutes each with buffer A at room temperature under gentle agitation. Sections were incubated with ligation solution for 60 minutes at 37 o C, then washed twice for 10 minutes each with buffer A at room temperature. The rolling ampli cationhybridization mixture was then added for 120 minutes at 37 o C.

Confocal imaging and quanti cations
The images were acquired using the Zeiss LSM 710 confocal laser-scanning microscope (Carl Zeiss AG, Germany) with a 20× air/dry or 63× oil objective and 10 µm z-stack scanning projections with a step interval of 1 µm, with a minimum resolution of 1200 x 1200 pixels.
For quanti cation, we compared two approaches, a traditional semi-manual quanti cation using ImageJ and an automated approach using the HCS Studio software associated with the Cell Insight CX7 highcontent imaging system (ThermoFisher Scienti c, Waltham, MA). For the semi-manual quanti cation, ImageJ was used to process each image into 8-bit greyscale images for each channel. The channel containing the PLA signal was thresholded until the PLA puncta were reliably isolated from the background forming a binary image. Overlapping PLA puncta were segmented using a watershed function and over/undersized puncta were excluded by de ning the expected size range of PLA puncta.
Size thresholding was adjusted for each cell line or experimental condition and estimated by measuring the diameter of isolated PLA puncta. The number of PLA puncta were then counted. Quanti cation of nuclei proceeds similarly; greyscale images were processed with a Gaussian blur, then thresholded as previously described with the additional of a "Fill Hole" function to optimize nuclear counting. Clumps of nuclei were again segmented, and the size range was de ned by measuring the area of the smallest and largest cell in the eld. The number of cells were then counted, and the summary result of PLA puncta/nuclei or PLA puncta/ eld was reported.
Analysis on the high-content imaging platform was performed by importing greyscale confocal images to the HCS Studio software (ThermoFisher Scienti c). Images were analyzed using the General Spot Measurement Tool to quantify the number of PLA puncta per eld. Thresholds for spot roundness, minimal and maximal spot intensity and size were comparable to those used in the semi-manual quanti cation.

Statistical analyses
The number of human brain donors (n) represented in each group is indicated in the gure legends. All data were analyzed using GraphPad Prism 9.0 (GraphPad Software Inc., San Diego, CA). An unpaired ttest was used to evaluate the two groups. The p value < 0.05 and lower was considered signi cant.

Results
Aggregated phosphorylated tau and ubiquitin distribution in AD hippocampus.
We performed a histopathological assessment and tested the speci city of antibodies in xed freeoating hippocampal and frontal cortex sections, respectively. Fluorescent staining of hallmark AD pathological structures in hippocampus tissue is shown in Fig. 1 and Supplementary Fig. 1. For most of the non-AD aging brain sections analyzed, tau aggregates were essentially absent, although a few cognitively intact brain sections occasionally had neuro brillary tangles (NFTs) (Fig. 1A and Supplementary Fig. 1A). In AD aging brains, abundant NFTs in neuronal cell bodies, neuropil threads and dystrophic neurites around neuritic plaques were observed, as is well known (Fig. 1B and Supplementary  Fig. 1B).
We evaluated the distribution of ubiquitin and p-tau in "normal" non-AD and in AD human brains (Fig. 2). In healthy brains and those with non-tauopathy disorders (like cerebral amyloid angiopathy), ubiquitin was detected primarily in puncta, mostly in a perinuclear distribution, likely representing physiological proteostatic mechanisms ( Fig. 2A, left panel). The degree of change in the abundance and distribution of ubiquitin in AD brain is striking; ubiquitin-stained twisted structures in occasional neuronal cell bodies in a pattern typical of neuro brillary tangles and linear areas resemble neuropil threads ( Fig. 2A, right  panel). Phosphorylated-tau immunohistochemistry in non-AD and AD brains was comparable to previous reports (42) and is shown in Fig. 2B. The overall level of immunoreactivity in AD samples was much higher (Fig. 2B, right panel). In view of a similar distribution of ubiquitin and phosphorylated tau, we next sought to demonstrate the existence of p-tau (Ser202, Thr205)-ubiquitin complex.

Assessment of direct interaction between ubiquitin and phosphorylated tau in-situ.
To date, in-situ PLA reports from the postmortem human brain remain scarce, in part due to technical di culties such as intrinsic tissue auto uorescence which is exacerbated during xation. We found that photobleaching using a broad-spectrum LED array can virtually abolish the auto uorescence (Fig. 3). The background observed with either 488 or 594-nm excitation (Fig. 3, left panel) was removed without tissue damage (Fig. 3B, right panel). Establishing a quiescent background is essential to obtaining speci c PLA labeling with adequate signal-to-noise ratio for precise quanti cation (Fig. 3B, right panel).
Since the hippocampal formation is vulnerable to NFTs we rst focused on evaluating the presence of ptau-ubiquitin complexes in this region. The approach to labeling the target interaction is outlined in Fig. 4A. Neurological control tissue from xed human post-mortem specimens had well-de ned PLA signals with minimal background staining primarily restricted to the nucleus (Fig. 4). In non-AD brains, the PLA signal corresponding to p-tau-ubiquitin complexes was sparse in areas of hippocampus (Fig. 4B). A clear increase of PLA signal was observed in the same areas in AD brains (Fig. 4C).
We quanti ed the relative number of uorescent foci, which we term "PLA puncta", in the frontal cortex (Fig. 5). Similar to the hippocampus, PLA puncta corresponding to p-tau-ubiquitin complexes was sparse in the frontal lobe of non-AD brains (Fig. 5A, left panel). Signi cantly greater levels of PLA puncta were observed in AD brains relative to non-AD brains (Fig. 5A, right panel: 996 ± 90 PLA puncta/ eld in AD vs. 363 ± 48 PLA puncta/ eld in neurological controls, n = 6, p < 0.0001) as determined by the quanti cation of the amount of PLA puncta per eld using ImageJ (Fig. 5B upper panel). Automated quanti cation using the HCS Studio software associated with the Cell Insight CX7 high-content imaging system showed a comparable increase in the PLA signal, 862 ± 110 PLA puncta/ eld vs. 185 ± 19 PLA puncta/ eld, n = 6 ( Fig. 5B lower panel). The approach to quantify PLA puncta using ImageJ is outlined in Fig. 5C and using the HCS Studio software in Supplementary Fig. 2.
Technical controls (Fig. 6A) using only the primary p-tau (Fig. 6A, left panel) or ubiquitin (Fig. 6A, right panel) antibodies displayed few and weak background PLA signals. For biological controls (Fig. 6B), we used brain sections from donors with cerebral amyloid angiopathy (CAA) without tauopathy or with low levels of tau pathology (n = 3). Sections with CAA showed PLA signals similar to those obtained in other non-AD samples (Fig. 6B, left panel) and much lower PLA signals than sections with severe tauopathy (Fig. 6B, right panel). The PLA signal in CAA did not associate with β-amyloid deposition (Fig. 6B, left  panel). Because PLA has been validated in cell models, the detection of p-tau (Ser202, Thr205)-ubiquitin complexes in iPSC-derived neurons was used as a positive control. PLA for the interaction of p-tau (Ser202, Thr205) with ubiquitin are primarily in neuronal processes as evidenced by their co-localization with beta III tubulin (Fig. 6C).

Discussion
This technical report presents an adapted uorescent in-situ PLA assay for use in human neuropathology which we applied to study ubiquitination of tau in postmortem human brains with AD. Prior uses of the uorescent PLA in human neuropathological specimens are scarce (43) and limited to bright eld preparations which have decreased sensitivity (44,45,46), but are not impacted by tissue auto uorescence. However, any of them have been focused on the understanding the dynamic of tauubiquitin complexes in AD, which is highly relevance in view of the contribution of tau ubiquitination in tau pathologies has not been completely clari ed. Our optimized photobleaching step abolishes the auto uorescence from lipofuscin and other pigments which accumulate in the soma. Alternative approaches to controlling auto uorescence, like treatment with solutions containing copper containing solutions or dark pigments (47,48), lead to tissue and/or antigen damage or mask speci c PLA puncta which may be undesirable when attempting to detect a truthful number of protein complexes or sensitively quantitate low-abundance protein modi cations or PPIs.
Further to a precise control of auto uorescence, proximity ligation assays procedures require selective/speci c and well validated antibodies In additional to pristine control of auto uorescence, proximity ligation assays procedures require selective/speci c and well validated antibodies. PLA has been criticized because the results use proximity as a surrogate for detecting PPIs (49). It is possible that proteins may be incidentally in proximity without directly interacting, but this is primarily a concern under non-physiological conditions, such as when proteins are arti cially overexpressed. It is likely that under the conditions present when evaluating brain tissue, the limitations of the assay are less problematic than in highly manipulated model systems. The use of appropriate controls is essential for the accurate interpretation of the results, including de ning the distribution and abundance of the individual proteins being studied.
The bright punctate signals resulting from in-situ PLA analysis are amenable to a range of quantitation approaches. Here, we found the technique was suitable for analysis in a high-content imaging system with results from human tissue. The coupling of PLA to high-content analysis greatly increases the rigor and e ciency of this method. In applying this technique, we found that phosphorylated tau associates with ubiquitin and accumulates in neurons in AD. This approach can be combined with histological or immunohistochemical stains to de ne the cell type, subcellular localization and other contextual features associated with a protein-protein interaction. This report shows the uorescent PLA technique can be a valuable tool to identify ubiquitin-substrate proteins, and while we focused on tau, the assay can be easily modi ed according to the protein-protein interaction or post-translational modi cation of interest.
Understanding the dysregulation of proteostasis in neurodegenerative disorders is an emerging research priority, as most neurodegenerative disorders are marked by the accumulation of protein aggregates of one form or another. Profound dysregulation of lysosomal function has been observed in Alzheimer's disease and ubiquitin-proteasome system (UPS) de ciencies have been also reported in AD, Parkinson's disease, frontotemporal dementia, and amyotrophic lateral sclerosis (50,51). In fact, as we show here and others have reported, the pathological accumulation of ubiquitin is remarkably abundant in AD (29). Polyubiquitination of proteins is best known for its role in facilitating protein degradation by the UPS and is accomplished by covalent crosslinking of a lysine residues in a chain of ubiquitin moieties to a lysine residue on a target protein. Variation in the linkage type of polyubiquitin chains can alter the fate of the tagged protein (52). There are several different linkage sites on ubiquitin -the best-known being K48polyubiquitination which targets proteins for degradation by the UPS pathway (53,54) and K6, K27, K33 which are related to immunity, cell proliferation, and DNA damage repair (55). Further, K63polyubiquitination directs proteins to the autophagy lysosomal pathway (ALP) but does not necessarily result in protein degradation.
The precise mechanism(s) at play here at not yet known and could be clari ed in future work by de ning the speci c ubiquitin linkages in phosphorylated tau aggregates. A form of aggregated tau in neuro brillary tangles in AD, Paired Helical Filaments (PHF)-tau, is suggested to be polyubiquitinated via not only K48 linkages, but also via non-canonical K6-and K11-linkages (28), whereas soluble tau can be ubiquitinated by K63 (27). The method presented in this report could be used to speci cally detect which lysine residues are modi ed, providing information regarding whether the modi cation will result in degradative or non-degradative outcomes. Despite the rapid metabolism of ubiquitin-tagged proteins in healthy neurons (56), our assay was able to detect ubiquitin conjugates in native conditions as evidenced by the PLA signals obtained in non-AD tissue. This likely indicates that under physiological conditions, the UPS controls tau synthesis, folding, and/or tra cking as well as degradation. The signi cant increase in PLA signal observed in AD brains demonstrates a defect in tau-related proteostasis in AD and is worthy of further study.

Conclusions
We conclude that ex-vivo PLA provides valuable information about protein complexes and PTMs while preserving spatial information and has some advantages compared biochemical and biophysical methods previously reported. This approach does not require transient protein overexpression, insertion of tags to facilitate immunoprecipitation or UPS inhibition to prevent the rapid metabolism of the ubiquitin-tagged proteins. The combination of PLA and high-content image analysis makes the approach rigorously quantitative and e cient. Incorporating this advanced molecular imaging technique into the repertoire of neuropathological tools will broaden the range of molecular information that can be derived from human brain tissue. Abbreviations PLA, Proximity Ligation Assay; AD, Alzheimer's disease; PPIs, protein-protein interactions; PTMs, posttranslational modi cations; NFTs, neuro brillary tangles; iPSC, Human induced pluripotent stem cell; UPS, ubiquitin-proteasome system; CA1, cornu Ammonis 1 ( rst region in the hippocampal circuit); DG, dentate gyrus.

Declarations
Ethics approval and consent to participate Brain tissue was obtained from the Vanderbilt Brain and Biospecimen Bank at Vanderbilt University Medical Center Nashville, Tennessee, USA (IRB# 180287). Written consent for brain donation was obtained from patients or their surrogate decision makers. Ethical approval was granted by Vanderbilt University Medical Center Institutional Review Board. The study has been carried out in accordance with The Code of Ethics of the World Medical Association (Declaration of Helsinki) for experiments involving human subjects.

Availability of data and materials
The datasets used in the current study are available from the corresponding author on reasonable request.

Competing interests
MSS has provided paid legal consulting and consulted for Raymond James and Associates on issues unrelated to this manuscript. He is also the chair of the DSMB for the REVISION trial. The other authors have no competing interests to disclose.  Large tau inclusions distinguish AD from aging human brains. This gure shows the early stage tauopathy seen in areas of human hippocampus in a "normal aging" (non-AD) brain without cognitive impairment compared to the advanced pathology seen in symptomatic AD. A) Lower and higher magni cation images of non-AD brain sections, n=4 and B) AD brain sections, n=4. The two-channel merged representative images were produced from 10 μm z-stack scanning projections with a step interval of 1 μm. Nuclei were stained with DAPI (blue) and β-amyloid and neuritic plaques, neuro brillary tangles and other tau aggregates were stained with Thiazine Red (red, see arrows). The scale bars are indicated. Abbreviations: CA1, cornu ammonis 1; DG, dentate gyrus.

Figure 2
Speci c immunolabeling revealed ubiquitin and phosphorylated tau in frontal cortex sections. A) Immunolabeling of ubiquitin (red) in non-AD brain (left panel) and AD (right panel), n=4. Neuritic plaques, neuro brillary tangles and other tau aggregates were stained with MX-04 (blue). B) Immunolabeling of ptau (Ser202, Thr205) (green) in non-AD brain (left panel) and AD (right panel), n=4 is shown. Neuritic plaques, neuro brillary tangles and other tau aggregates were stained with Thiazine Red (red). The two-channel merged representative images were produced from 10 μm z-stack scanning projections with a step interval of 1 μm. The scale bars are indicated.   In-situ PLA detected protein complexes between p-tau and ubiquitin in hippocampal sections from non-AD and AD human brains. A) Schematic representation of the PLA. First, a pair of well-validated primaries antibodies binds target proteins. Second, a pair of secondary species-speci c antibodies conjugated to complementary oligonucleotides (ssDNA, MINUS and PLUS) recognize the primary antibodies. If targets are in proximity (≤ 40 nm), a circular ssDNA will form. A ligase facilitates the hybridization of oligonucleotides to form a double strand acting as a template for rolling circle ampli cation. Finally, a polymerase generates an ampli ed rolling circle product that is hybridized by uorescently labeled probes to generate a speci c PLA signal (red puncta). B) Proximity ligation puncta indicated by arrows represent the protein complexes between p-tau (Ser202, Thr205) and ubiquitin found in areas of hippocampus in (B) non-AD, n=3 and (C) AD, n=3 sections. The three-channel merged representative images were produced from 10 μm z-stack scanning projections with a step interval of 1 μm. Nuclei were stained with TO-PROTM3 (blue), and tau pathology and β-amyloid aggregates were stained with MX-04 (green). The scale bars are indicated. Figure 5 p-tau (Ser202, Thr205) modi ed with ubiquitin was signi cantly higher in AD frontal lobe tissue compared to non-AD. Quanti cation of p-tau (Ser202, Thr205) modi ed with ubiquitin in frontal cortex sections from non-AD and AD human brains. A) Proximity ligation puncta (red clusters) indicated by arrows represent the protein complexes between p-tau (Ser202, Thr205) and ubiquitin found in non-AD (left panel) and AD (right panel), n=6. Nuclei were stained with TO-PROTM3 (blue) and tau and β-amyloid Technical and biological controls validated the in-situ PLA technique. A) As technical controls for the PLA probes and procedure, PLA puncta (red) were evaluated while excluding one of the primary antibodies to assess non-speci c background labelling. Representative images show the background PLA signals when using only the p-tau (Ser202, Thr205) antibody (left panel) or ubiquitin antibody (right panel). B) As a biological control, we evaluated PLA puncta (red) detected in brain sections with cerebral amyloid